What issues were there in 3E that 3.5 fixed?
Rangers and bards were made less garbage, if I recall correctly.
Nerfing
haste was probably a good call, just because of action economy.
Most of the other changes were fiddly and/or dumb. Messing with buff durations didn't make the game noticeably better, for instance, but it didn't make things worse, either - just different.
What issues were there in 3.5 that Pathfinder fixed?
...racial ability scores, maybe?
PF compared to 3.5 is mostly just rearranging the chairs. 3.5 had a lot of acknowledged problems, none of which PF actually fixed. While the skill system is a mild improvement, it's still a lot of bookkeeping and has its own set of weird results.
What issues were there that 3.5 made worse?
I don't recall seeing anything that made me actively prefer 3e over 3.5. As I said, there were fiddly changes, but there were enough good changes (bard, ranger) that it was worth dealing with the minor changes.
What issues were there that Pathfinder made worse?
At first it seemed like a fair improvement. At this point, though, the system is bloated as all hell, and it has way too many fiddly bits.
What have you house ruled in your 3E / 3.5 / Pathfinder game? What have you rolled back to a previous version?
Wrote a whole list of homebrew classes, banned all the original classes, ripped out the skill system, rewrote feats, wrote new spell systems, reworked equipment and magic items, made significant modifications to how wealth works, went to a 4e-style monster design paradigm, changed how HP and damage scale across the board...
I think at this point the only things that my games have recognizably in common with 3.5 are (1) it's vaguely d20-based, (2) we have the six traditional D&D ability scores (plus some others), and (3) we have the standard D&D races, along with a whole bunch of others.
You could not bring a vanilla 3.5 character into my games. Wouldn't even begin to work.